BIOMEDICAL RESEARCH EXPERIENCES

FOR ENGINEERING MAJORS

2005

We would like to announce a new summer research program for Tufts undergraduates (U.S. citizen or permanent resident). It’s called Biomedical Research Experiences for Engineering Majors, or BREEM. This NIH-funded program is designed for Tufts students who are majoring in engineering or computer science and are interested in how these disciplines can be applied to biomedical research. Ten students will work individually with faculty on a research project over the summer, for a minimum of ten weeks. Accepted students will receive a stipend of $5,160 and up to $750 to defray research costs.

Students must first identify and contact a faculty mentor. The attached list describes some of the available research opportunities, but you are not limited to these faculty as mentors. The application deadline is March 11, and should include the materials listed in the application packet. Once accepted to the program, you will work with the faculty mentor during the spring semester to develop a proposal for the summer project. This is due May 15. Depending on the needs of the project, we will also pair you with a mentor from the School of Engineering. The summer experience will include a seminar series given by Tufts investigators actively engaged in research using biomedical engineering or analyzing complex biological systems with computer modeling.

SUMMER PROGRAM TIME COMMITMENT: May 30, 2005 – August 5, 2005

If you have questions, please contact the program directors listed below:

Prof. Claire Moore

SacklerSchool of Graduate Biomedical Research

617-636-6935

Prof. Peter Wong

School of Engineering

617-627-2985

Research Opportunities, 2005

Alphabetically Listed by Research Mentor

Anselm Blumer (Engineering) and Alan Kopin (Sackler): The long range goal of
this project is to identify new genes involved in obesity and diabetes. We
are looking for someone with scripting skills to write a script to submit
queries and compile results from NCBI's homolog detection Web site
(³homologene²):

We would like to be able to analyze the single disrupted gene in each of
~5,000 mutant Drosophila (fruit fly) strains to determine if the
corresponding protein is conserved in mice and humans. This subset of
mutant flies will be used for behavioral screening aimed at identifying
novel genes relevant to the pathophysiology of obesity and diabetes. The
output should be compiled in a file that can be imported into a spreadsheet
and ranked according to degree of homology with corresponding mammalian
proteins. This analysis should narrow the number of flies to be screened in
behavioral assays to a more manageable amount.
617-627-3651 and

Andrew Bohm: Protein crystallography, the primary technique employed by my laboratory, lies at the interface between biochemistry and experimental physics. Data analysis is very computer intensive, and we are interested in improving existing methods of collection of diffraction data, molecular model building, and molecular dynamics refinement. We also want to build small devices to facilitate sample handling, work out transformation matrices so that the coordinate systems used by some of our hardware and software could be inter-converted, and write drivers so that joysticks and other 3D interface devices could be productively used in conjunction with our molecular modeling software. . 617-636-2994

Caroline Cao: Augmented reality simulators, not unlike many commercially available videogames, are being used to train surgical skills. We are interested in exploring the use of augmented reality for training dynamic surgical skills, and developing a multi-dimensional metric to quantify the skill

performance. 617-627-2484

ase.tufts.edu/faculty-guide/faculty.asp?id=ccao03&deptId=mecheng

Brent Cochran: The primary research focus of my laboratory is to understand how peptide growth factors are able to regulate cell growth and differentiation. We have encountered several problems that require computer science solutions. First, our research requires statistical analysis of the large data sets generated using microarray technology to determine gene expression. We need to use real and simulated datasets to compare the performance of several methodologies for the analysis of this microarray data. In addition, we would like to use computational linguistics to develop a text mining project tool which can construct biological pathways. Another project involves the extension of our pattern matching algorithms to extract phosphorylation site information and cellular localization information from Medline abstracts. 617-636-0442

James Dice: My research interest is in the lysosomal pathway of proteolysis that is activated when cells are stressed. The activity of this protein degradation pathway, chaperone-mediated autophagy, can be used as an indicator of cell stress to monitor cell response to different bioengineered materials. In addition, I am interested in how cells take up and degrade extracellular matrix materials such as collagens that are used as support matrices for artificial organs. 617-636-6707

Kathy Dunlap: Research in our laboratory focuses on the molecular and biophysical mechanisms underlying the modulation of voltage-dependent calcium channels and on identifying the functional consequences of such modulation for synaptic transmission in the nervous system. We use neurophysiological methods to understand how mutations in these channels lead to neurological diseases. We are interested in someone who could help us develop an efficient means of electrically stimulating cells in culture. 617-636-4942

Eddie Goldberg: We work in Bio-Nanotechnology. We redesign genes to make bio-molecular carpentry kits to develop a technology for massive parallel manufacture of new materials. Biomimetic fabrication of functional protein nanostructures requires control of self-assembly. The basic constructs are made of stiff, rugged protein rods of 10-100nm, to which molecular moieties (nanocrystals to individual proteins) are attached at specific sites for function. Site placement need not be monotonous and can form arrays on matrices, or open frameworks, in 1, 2 and 3 dimensions. Composite materials and devices are hierarchically assembled, from nanometer to macroscopic level as porous, non-random, functional materials for various biological and non-biological applications, from light structural reinforcement and boundaries, to composite materials for separation, catalysis, tissue

engineering and diagnostics. Reference: Hyman, P., Valluzzi, R. and E. Goldberg. 2002. Design of protein struts for self-assembling nanoconstructs. Proc. Natl. Acad. Sci. USA 99:8488-8493. 617-636-6754

Ronald Hammer: Mesocorticolimbic circuits regulate sensorimotor gating in normal human brains and dysfunction produces sensorimotor gating deficits in schizophrenia. The relevant neural pathways involving various neurotransmitters have been studied, as have molecular processes involved in signal transduction underlying sensorimotor gating. The interaction of these circuits, signals and processes could be modeled in such a way as to predict behavioral outcomes and develop testable hypotheses. The student will develop a model to represent this process, and will test the model against experimental paradigms using acute and chronic administration of various receptor agonists and antagonists that affect sensorimotor gating.

617-636-8936

Daniel Jay: Our work on protein function in neurogenesis and cancer metastasis uses high-throughput functional screens that require knowledge of microfabrication and bioinformatics, mathematical modeling of how cells and growing axons move and how force is integrated and converted into cell movement, and biotechnology development using light to inactivate proteins in living cells. 617-636-6714

Alan Kopin (Sackler): Our research interests are focused in molecularendocrinology with an emphasis on G protein-coupled receptors (GPCRs). Investigations are aimed at defining structure-function relationships of GPCRs including the identification of ligand binding determinants and the mechanisms of signal transduction (ligand and/or mutation induced). Based on this expertise, the laboratory has developed molecular tools to expedite GPCR drugdiscovery. We would like to conduct high throughput screening for drugs that affect GPCRs. We are looking for a student who can adapt existing robotics for use with our assays. The student would need to also find a suitable comentor in Engineering. (617) 636-4834

Kyongbum Lee (Engineering): Our research is aimed at better understanding ata systems level the metabolic regulation in cells and tissues in vivo and in vitro in order to optimize the performance of tissue engineered therapeutic devices as well as elucidate mechanisms of disease. Current projects include metabolic control of adipose tissue expansion, optimization of stem cell differentiation on nano-crystalline ceramics, and development of novel biosensors for real-time metabolite detection. 617-627-4323 ase.tufts.edu/chemical/faculty-staff/faculty/lee.asp

Natesa Pandian: Our work focuses on 3D ultrasound imaging of the heart in health and disease. Specific projects include determining volume:mass relations of the left ventricle (the main pumping chamber) in heart failure patients.

617-636-6151

Susan Roberts: We study the dietary composition factors and eating behaviors that cause overeating and weight gain at different stages of life. We are very interested in collaborating with engineers to create inconspicuous ways of measuring or verifying dietary intake and physical activity. Projects in our research group would involve the development and validation of a remote data collection system for food intake and body weight, perhaps by creating a radiowave communication network for data collection within subjects' houses.

617-556-3238 hnrc.tufts.edu/scientists/people/sroberts.php

Satyapriya Sarkar:Our research involves the structure and function of muscle proteins in the Ca 2+ regulation of vertebrate striated muscle contraction. We use a multidisciplinary approach to study how biological motion in striated muscle is regulated by “information transfer” through multi protein complexes. We are also interested in how this process is correlated with the structure and function of the genes encoding these proteins.Computer assisted analysis of nucleotide and amino acid sequences is an important component of these studies. We also use biophysical approaches such as fluorescence enhancement and/or decay of appropriately labeled native and mutant proteins circular dichroism and isothermal calorimetry to study protein – protein interactions involved in this biological system. The ongoing projects deal with the mechanistic aspects of muscle biology and physiology. Participation in these projects should expand the perspective of engineering students in biological 617-636-2931

James Schwob:My laboratory is interested in using transplanted stem cells or activating endogenous ones to repair or regenerate damaged tissues. We focus on the mammalian peripheral olfactory system because it is neural tissue that is uniquely able to repair itself after injury, which reflects, in turn, the retention of an active population of neurocompetent stem cells
in the olfactory epithelium (OE) throughout life. [Its remarkable capacity for regeneration also makes it a uniquely powerful model for studying the development of the nervous system]. A particular challenge is the need to expand and manipulate the stem cells in vitro in order to engineer tissues for use in repair. In particular, three-dimensionality is an underappreciated aspect of the in vitro assembly of properly differentiated tissues. We are collaborating with Dr. David Kaplan, Chair of Biomedical Engineering, in attempts to construct 3-D scaffolds, decorated with relevant biomolecules, to compel the regulated differentiation of neural stem cells from the OE and the assembly of a well-ordered, reconstituted epithelium in vitro.

617-636-6626

Barry Trimmer & David Kaplan: A project in our group would involve the design & fabrication of biologically inspired, soft-bodied robots.Most of today’s crawling robots are constructed with hard materials, motorized actuators and rigid “skeletons” that have a limited range of movements. However, most crawling animals have soft-bodies that use combinations of fluid (hydrostatic), and tissue pressure (muscular hydrostats), to provide stiffness against which muscles can work. Such movements are particularly interesting from a neural control perspective. With no easily defined joints, each muscle contraction has the potential to move the body in any plane and to cause crumpling, rotation and complex bending; little is known about how such behaviors are organized. None of the current multisegmental crawling robots adequately mimic the remarkable abilities of soft-bodied animals, for example they do not climb and do not have the static and dynamic stability of caterpillars. In this collaborative project we will begin to design and fabricate soft bodied robots based on principles learned from our kinematic and physiological studies of the tobacco hawkmoth (Manduca sexta) caterpillar. These robots have potential applications in navigating pipelines and wiring conduits or in the exploration of intricate biological structures such as guts, blood vessels and air tubes. Specific topic areas include the design and fabrication of instruments to measure biomechanical properties; measurement of mechanical performance by caterpillars; designing neurally inspired control systems; testing novel actuators (such as artificial muscles), and modeling of motor patterns or deformations by finite element analysis.

617-627-392 Ase.tufts.edu/BIOLOGY/faculty/bios/trimmer/trimmer.html

Paula Watnick: My laboratory studies the genetic basis of adhesion of pathogenic bacteria to surfaces. We are currently in the process of designing flow cells that we can use to study this process microscopically. We wish to more closely simulate the natural forces that these bacteria would encounter in the environment and upon colonizing tissues and analyze how gene expression patterns change during this process. 617-636-2545

TUFTS BIOMEDICAL RESEARCH EXPERIENCES

FOR ENGINEERING MAJORS

APPLICATION

Name:______

Expected Graduation Year:______

Major(s):______

______

Minor(s):______

______

Academic Advisor(s):______

______

Mailing Address:______

______

______

Telephone:______

Email Address:______

Mentor with whom you are applying:______

Names of people submitting ______

letters of recommendation on your behalf:

______

Applicant’s signature affirming agreement to ______

program requirements

Applicant Requirements

  • You must have a GPA of 3.0 or greater.
  • You must be a Tufts sophomore, junior or senior during the 2005-2006 academic year and a U.S. citizen or permanent resident.
  • You must submit your application following the instructions described below.
  • You and your mentor must agree to the expectations outlined below.

Application Procedure

Applicants must submit 2 copies of the application to Dr. Peter Wong, Anderson 109, or send it in .pdf format via email to y 11AM on Friday, March 11.

The completed application contains the following:

  1. Completed Application Form.
  1. College transcript. An unofficial copy printed from SIS online is acceptable. Transfer students should include their transcript from their former institution.
  1. A description of your project (not more than 1000 words). Please include the following components:
  • A description of the question to be explored and how engineering or computer science will be applied to this biological problem
  • A brief statement as to why this question is important
  • Project location

4. A personal statement (not more than 1000 words). This essay should address your

interest in exploring the connections between engineering and biomedical science and

your plans for the future. If you have had previous research experience, please describe

it.

5. A letter of collaboration written jointly by the student and mentor, signed by both.

The letter should include the following components:

  • Explanation of how the student’s and mentor’s research interests are similar
  • Proposed timeline of events
  • Expectations for those involved with the project

Completed applications must be submitted by 11AM on Friday, March 11, 2005. Any applications received after that date will be considered only if space is available.

Letters of Recommendation

Applicants must submit at least one and no more than two letters of recommendation. At least one of these letters must be from a current Tufts faculty member.

These letters may be submitted with the application or sent separately to Dr. Peter Wong, School of Engineering, Anderson 109, or by e-mail to . All letters must be received by 11 AM on Friday, March 11.

Student Expectations

Employment

  • Students may not be otherwise employed during the summer program without consent from the Program Directors before the application is submitted.
  • Enrollment in courses relevant to the research project is permitted, but only with the express consent of the Program. Plans for Summer School should be mentioned in the application; questions concerning Summer School should be addressed before application is made.

Residency

  • Students may work at any one of Tufts’ three Massachusetts campuses (Medford/Somerville, Boston, Grafton) or at one of Tufts’ affiliated hospitals or clinics.
  • Recipients must arrange their own housing.
  • On-campus housing can be arranged if necessary.

Research Project

  • Must be supervised by a Tufts faculty member.
  • Must involve an application of engineering or computer science to biomedical research.
  • The project will conclude with written and oral presentations.
  • A written report on the results of the summer research to one’s mentor and to the Program Directors (3-5 pages).
  • You will be asked to participate in a poster session put on by the Program, and in the Tufts Undergraduate Research and Scholarship Symposium in the Spring of 2006.

Mentor Expectations

A core component of the program is the joint commitment between faculty/clinical mentors and students during the research process. Faculty mentors are expected to work with the students to design a project that is sufficiently well-defined so that meaningful progress can be made over the summer session. Development of a timetable and milestones is encouraged to ensure that the project can be managed within the time frame of the program.

During the summer internship period, the mentor has the following responsibilities:

  • Train the student in the necessary skills or assign a competent member of the laboratory to this role
  • Help the student understand how the project fits in the broader scope of the laboratory’s research goals and how the research is addressing important questions in the mentor’s field
  • Supervise the student’s research project, and if necessary, assign a graduate student or post-doctoral research associate for day-to-day interactions with the intern
  • Assist in preparation of the written proposal, the final written report, and the poster presentation
  • Provide an evaluation of the student at the end of the summer.
  • Actively participate in the poster session and in the Tufts Undergraduate Research and Scholarship Symposium (see ase.tufts.edu/symposium).

1